Towards Improved Ribosomal Profiling Protocol for Large Scale In vivo mRNA Translation Study

Translational control is a central regulatory step of gene expression that occur in all living cells all the time. Ribo-Seq is a novel experimental approach for studying mRNA translation, which enables reconstructing the ribosome densities on thousands of translated transcripts at nucleotide resolution in vivo. This method should enable answering, for the first time, some of the most fundamental biological questions related to mRNA translation regulation; in addition, it should accelerate developing gene expression models and engineering approaches. However, the current protocol of Ribo-Seq introduces various non-trivial biases that are yet to be fully understood. Here we will describe the study of Ribo-Seq using a Small RNA kit (NEBNext); based on the analysis of the Ribo-Seq data, we demonstrate some sources for biases and discuss possible solutions.